Yes - the ancient world was highly prone to warfare, so it was inevitable that Greek colonists would sometimes find themselves at odds with native populations. An example that springs to mind is the Greek colony of Tarentum (modern Taranto) in southern Italy. The Tarentines (and their allies in the region of Italy known as magna Graecia - great Greece) felt threatened by the growing power of Rome in the north, and went to war with the Romans in the early third century BC, famously calling in king Pyrrhus of Epirus to assist them in their (ultimately unsuccessful) struggle.